EENdb - Utilities  >  ZFP construction strategies
This page describes and compares the ZFN/ZFP construction strategies and methods.
For web-tools and resources of ZFN/ZFP engineering, see the page of Engineering Resource.

List of ZFP construction strategies
Direct assembly MA
(Modular Assembly)
MA considers each zinc fingers as an independent module, and directly assembles 3 (or more) fingers according to the target site sequence into a ZFP/ZFN.
There are many sets of modules for selection.
> Quick and straightforward.
> Reported low success rate.
9843940 (Original)
17406455 (Protocol)

ZFNs by MA
(Context-Dependent Assembly)
CoDA is also a direct assembly strategy, but the 3 fingers, especially the relatively important F2, were selected from effective ZFPs by OPEN, which showed robust efficiency in different contexts. > Quick and easy.
> Reported ~50% success rate.

ZFNs by CoDA
(Named by EENdb)
S. Wolfe's group (authors of "PRS") also developed a 2-finger modular assembly system mainly covering GRNNYG. Combined with 1-finger modules, this system can be used to construct 3-finger or 4-finger ZFPs/ZFNs. > Quick and easy.
> Reported ~80% success rate.

ZFNs by "2F-MA"
Screening-based OPEN
(Oligomerized Pool ENgineering)
OPEN employs a two-step screening. the first step is to establish pre-screened pools of single zinc fingers targeting a specific triplet from a pool of nearly randomized oligos by using a phage-display system; The second step is to assemble 3 pre-screened pools into a ZFP pool to perform the second screening. > Time- and labor-consuming for the first screening step, or need to reuqest the pre-screened pools.
> Reported high success rate.
19798082 (Protocol)

("Partially-Randomized Screening")
(Named by EENdb)
"PRS" relies on one-step or two-step screening. The initial zinc finger pools (library) are designed to be patially randomized regarding the coding potentials for each zinc finger, some residues are fixed (especially for G and A in the triplet targets) and others are randomized.
"PRS" is named by EENdb; some review articles call it as "B1H" strategy, but it may cause confusion with the ZFP screening method.
> The size of the library for screening is relatively more controllable and easier to handle than OPEN.
> Reported high success rate.

ZFNs by "PRS"
Commercial service Sangamo 2-finger module based assembly and/or screening strategy is initially developed by A. Klug and M. Isalan (reviewed by 20478078). The non-public, commercial strategy used by Sangamo BioSciences Inc. (or Sigma Aldrich Inc.) is mainly based on this work.
ToolGen Inc. also employs a public 2-finger based MA strategy (noted as "MA(2F)" by EENdb).
ZFNs by Sangamo

Relationship of different strategies

This figure is modified from 22049679 (A review in Chinese).

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